Dear all

Perhaps a bit off of theme, just an example about resolution cut-off

mean I/sigma(I) = 2 for dmin = 3.35 A

(please have a look at the attached pdf)

I would trust in I/s(I) = 2 (in this case it worked), but why not to  
determine what is information after the model has been refined to some  
extent using lower I/s(I) and then cutting the resolution by 0.05-0.1 A?

Delta R and (from procheck) Avg-G factors did well. Note that Rfree  
improved by using data from higher resolution.

Perhaps if Rmeas or Rpim were bad at that resolution (3.35 A) the  
story would be different.

Best regards,

Horacio





Quoting John R Helliwell <[log in to unmask]>:

> Dear Jacob,
> As an editor I am always mindful that an article is finally under the
> authors' names. That said the reader always deserves to know at what
> diffraction resolution average intensities (cease to) exist. The usual
> statistical practice to do that is to use a given quantity's (ie in
> this case a reflection intensity) sigma.
>
> Good effort is made in data processing programs to protect the quality
> of the estimate of each reflection intensity's sigma notably the chi
> square test.
>
> Thus I request that the diffraction resolution where <I/sig(I)>
> crosses 2.0 is quoted in the article, if it is not there already. I
> agree that 2.0 is arbitrary but it is more 'lenient' than the usual
> '3sigma' statistical test.
>
> Sometimes the title or abstract has to be changed to follow this
> criterion; eg 'The structure of xxx is determined to 2.4 Angstrom
> resolution' type of title has to be consistent with the above
> criterion.
>
> I do not follow an 'Rmerge must be less than x% rule'.
>
> I think the above follows reasonable general statistical practice,
> whilst permitting authors reasonable freedom, and also protects the
> (more innocent) readers of articles.
>
> I am aware that the 'correlation coefficient' between randomly
> portioned parts of data sets is being increasingly discussed, this
> parameter also having general statistical validity. I am monitoring
> discussion on this carefully. It has long been a good way of assessing
> the statistical quality of anomalous differences for example; to my
> knowledge introduced by Michael Rossmann many years ago.
>
> Best wishes,
> John
>
>
> On Fri, Jan 27, 2012 at 5:55 PM, Jacob Keller
> <[log in to unmask]> wrote:
>> Clarification: I did not mean I/sigma of 2 per se, I just meant
>> I/sigma is more directly a measure of signal than R values.
>>
>> JPK
>>
>> On Fri, Jan 27, 2012 at 11:47 AM, Jacob Keller
>> <[log in to unmask]> wrote:
>>> Dear Crystallographers,
>>>
>>> I cannot think why any of the various flavors of Rmerge/meas/pim
>>> should be used as a data cutoff and not simply I/sigma--can somebody
>>> make a good argument or point me to a good reference? My thinking is
>>> that signal:noise of >2 is definitely still signal, no matter what the
>>> R values are. Am I wrong? I was thinking also possibly the R value
>>> cutoff was a historical accident/expedient from when one tried to
>>> limit the amount of data in the face of limited computational
>>> power--true? So perhaps now, when the computers are so much more
>>> powerful, we have the luxury of including more weak data?
>>>
>>> JPK
>>>
>>>
>>> --
>>> *******************************************
>>> Jacob Pearson Keller
>>> Northwestern University
>>> Medical Scientist Training Program
>>> email: [log in to unmask]
>>> *******************************************
>>
>>
>>
>> --
>> *******************************************
>> Jacob Pearson Keller
>> Northwestern University
>> Medical Scientist Training Program
>> email: [log in to unmask]
>> *******************************************
>
>
>
> --
> Professor John R Helliwell DSc
>